The combination of ultrastructural technology and other disciplines should favor the development of soil science and microbiology in more intuitive and microscopic directions. Interactions between the soil and microorganisms occur all over the soil interface, which strongly affects the transportation of environmental pollutants. In this study, the importance of micro-area analysis was carefully elucidated for the ultrastructural study of the interfaces between soil and microorganisms. The methods for sample preparation were also briefly introduced for use in the visualization of ultrastructural features by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) coupled with energy dispersive X-ray analyses (EDX), high-angle annular dark-field (HAADF), and electron diffraction (ED) analysis. These techniques were further employed to observe bacterial morphology and its intracellular organization, determine the nature of interactions between bacteria and soil components at their interfaces, detect their composition, and study the interactions between bacteria and environmental pollutants under environmental stress. Corresponding studies revealed that bacteria easily attach to the surfaces of soil particles, accelerating the biodegradation and biotransformation of pollutants by adjusting their cell surface properties. Furthermore, previously published research showed that the co-culture of different bacteria favored the biodegradation process, which would be helpful for elucidating the ultrastructural mechanisms at micro-interfaces while tracking trends in the transfer of environmental pollutants. In conclusion, the application of SEM and TEM should favor the development and application of bioremediation technology for contaminated soils and sediments.